Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Applicant's preliminary amendment filed on June 11, 2026 is acknowledged. Claims 2, 4, 5, 8, 9, 11, 13-16, 19, 21, 22, 29-33, 35, 38, 40, 41, and 43-56 have been canceled. Claims 1, 18, 39, and 42 were amended. Claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, 37, 39, and 42 are pending.
Election/Restrictions
Applicant's election with traverse of Group I (claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, and 37) in the reply filed on June 11, 2026 is acknowledged. The traversal is on the ground(s) that it would not be unduly burdensome to perform a search on all of the claims together in the present application. This is not found persuasive because the instant application claims priority to a 371 application and thus the requirement for restriction is not because the inventions are independent or distinct and there would be a serious search and/or examination burden. Instead, the restriction is on the grounds that Groups I and II lack unity of invention because even though the inventions of the groups require the technical feature of the RNA trans-splicing molecule of claim 1, the technical feature is not a special technical feature as it does not make a contribution over the prior art in view of Gruber et al. (reference of record) and Lemaitre et al. (reference of record).
The requirement is still deemed proper and is therefore made FINAL.
Claims 39 and 42 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on June 11, 2026.
Claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, and 37 are examined on the merits herein.
Priority
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Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on August 1, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
The drawings were received on March 25, 2026.
The drawings are objected to because Figures 3A and 3B are blurry and hard to decipher. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The substitute specification filed on March 25, 2026 has been entered.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because the abstract uses the phrase “This invention relates to” which can be implied. In addition, the abstract reads “(ill)” and should read “(iii)”. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
The disclosure is objected to because of the following informalities:
Page 4, line 36 refers to “green blocks”; however, color drawings were not submitted with the application.
Page 11, second paragraph: a period is missing at the end of the sentence.
Appropriate correction is required.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. See page 26, line 40.
Claim Objections
Claims 1, 23, and 24 are objected to because of the following informalities:
Claim 1 recites the abbreviation HERV. The abbreviation should be clearly written out at the first occurrence in the claim and should be followed by the abbreviation in parentheses.
Claim 23 recites in part “comprising the nucleic acid sequence of SEQ ID 2NO: 13”. It appears that there is a typographical error and Applicant may have intended for claim 23 to recite “SEQ ID NO: 13” instead (remove “2”).
To improve the grammar of claim 24, the word “the” should be added before the phrase “trans-splicing domain”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 27 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 27 recites the limitation "the binding domain" in lines 2 and 3. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend the claim to recite “the binding region” (emphasis added) in both instances.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 28, 34, and 36 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 28 is drawn to a nucleic acid encoding an RTM according to claim 1. Claim 1 is drawn to an RNA trans-splicing molecule (RTM) comprising a binding region specific for a HERV pre-mRNA, a trans-splicing domain, and a coding sequence for a suicide protein. Dependent claim 28 substitutes RNA with DNA. Thus, the dependent claim no longer includes all of the limitations of the claim from which it depends.
Claims 34 and 36 are included in the rejection because the claims depend on claim 28.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, and 37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, and 37 are drawn to the provision of a genus of binding region sequences comprising a variant of SEQ ID NO: 4 and a genus of nucleic acid sequences comprising a variant of SEQ ID NO: 13 or a variant of SEQ ID NO: 15. The specification discloses the following:
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[page 1, first paragraph].
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[page 1, second to last paragraph].
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[page 8, fourth paragraph]. Thus, the claims encompass a broad genus of binding region sequences comprising a variant of SEQ ID NO: 4 that bind to HERV pre-mRNA in a cell and a broad genus of nucleic acid sequences comprising a variant of SEQ ID NO: 13 or a variant of SEQ ID NO: 15 that mediate trans-splicing of a suicide gene.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof.
The specification envisions the following:
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[page 8, second and third paragraphs].
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[page 14, second paragraph].
The specification discloses the following sequences:
SEQ ID NO: 1 (HERV-K target sequence of binding region (DNA))
SEQ ID NO: 2 (HERV-K target sequence of binding region (RNA))
SEQ ID NO: 3 (reverse complement of HERV-K target sequence (DNA))
SEQ ID NO: 4 (reverse complement of HERV-K target sequence (RNA))
SEQ ID NO: 5 (modified reverse complement of HERV-K target sequence (RNA))
SEQ ID NO: 6 (HSV Thymidine Kinase (HSV-tk) amino acid sequence (AAC16235.1))
SEQ ID NO: 7 (HSV Thymidine Kinase (HSV-tk) coding sequence (AF057310.1))
SEQ ID NO: 8 (modified HSV Thymidine Kinase (HSV-tk) amino acid sequence)
SEQ ID NO: 9 (modified HSV Thymidine Kinase (HSV-tk) coding sequence)
SEQ ID NO: 10 (spacer sequence)
SEQ ID NO: 11 (P2A cleavage sequence)
SEQ ID NO: 12 (Trans-splicing domain sequence)
SEQ ID NO: 13 (RTM sequence)
SEQ ID NO: 14 (coding DNA sequence for RTM SEQ ID NO: 13)
SEQ ID NO: 15 (RTM sequence with modified HSV-tk coding sequence)
SEQ ID NO: 16 (coding DNA sequence for RTM with modified HSV-tk coding sequence SEQ ID NO: 15)
SEQ ID NO: 17 (nucleotide sequence encoding P2A peptide).
No description is provided of any other binding region sequences comprising a variant of SEQ ID NO: 4 or any nucleic acid sequences comprising a variant of SEQ ID NO: 13 or a variant of SEQ ID NO: 15.
Even if one accepts that the example described in the specification meet the claim limitations of the rejected claims with regard to structure and function, the example (SEQ ID NO: 5) is only representative of one variant of SEQ ID NO: 4. The result is not necessarily predictive of other binding region sequences or nucleic acid sequences falling within the broadly claimed genus not limited to any particular structure. Thus, it is impossible for one to extrapolate from the limited example described herein those binding region sequences or nucleic acid sequences that would necessarily meet the structural/functional characteristics of the rejected claims.
Koller et al. (Molecular Therapy – Nucleic Acids 2014) discloses that successful trans-splicing in an authentic, endogenous environment requires a highly functional and specific RTM to provide a therapeutically relevant level of correction and to exclude unspecific splicing events due to the relative underrepresentation of the target molecule [page 1, left column, second paragraph]. Koller et al. also discloses that the binding domain (BD) is very variable, and even slight variations can change the efficiency of the trans-splicing (TS) process significantly [page 1, right column, last paragraph].
The prior art does not appear to offset the deficiencies of the instant specification in that it does not describe a set of binding region sequences comprising a variant of SEQ ID NO: 4 that bind to HERV pre-mRNA in a cell and a set of nucleic acid sequences comprising a variant of SEQ ID NO: 13 or a variant of SEQ ID NO: 15 that mediate trans-splicing of a suicide gene.
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 1, 3, 6, 7, 10, 12, 17, 18, 20, 23-28, 34, 36, and 37.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3, 10, 17, 18, 28, 34, 36, and 37 are rejected under 35 U.S.C. 103 as being unpatentable over Gruber et al. (Molecular Oncology 2013; reference previously cited by the Examiner) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner).
Regarding claims 1 and 3, Gruber et al. designed RNA trans-splicing molecules (RTM) specifically binding the pre-mRNA of SLCO1B3, a marker gene in epidermolysis bullosa associated squamous cell carcinoma (EB-SCC). Specific trans-splicing, results in the fusion of the endogenous target mRNA of SLCO1B3 and the coding sequence of the suicide gene, provided by the RTM. Further, Gruber et al. teaches that targeting tumor marker genes by RNA trans-splicing is a promising means to induce tumor cell-specific death [abstract]. Gruber et al. teaches that a trans-splicing reaction is facilitated by RNA trans-splicing molecules (RTMs) consisting of a binding domain (BD) for gene targeting, a splicing domain for efficient trans-splicing, and a coding domain comprising the sequence to be introduced [page 1057, left column, second paragraph].
Regarding claim 10, Gruber et al. teaches that to further evaluate the specificity of RTMs in a suicide gene therapy approach, the binding domain (BD) from RTM_1 was cloned into the suicide RTM plasmid containing the thymidine kinase (tk) sequence from herpes simplex virus (HSV) [page 1061, left column, first full paragraph].
Regarding claims 17 and 18, Gruber et al. teaches an RTM construct containing the binding domain (vertical lines), branch point (circle), poly pyrimidine tract (rectangle), 3’ splice site (inverted triangle), and HSV-tk w/o ATG in 5’ to 3’ direction as shown in Figure 2A (reproduced below). It is noted that the 3’ss (3’ splice site) is a splice acceptor site.
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Regarding claim 28, Gruber et al. teaches that one of the most efficient BDs, evaluated in our fluorescence-based screening system, was cloned into the pIRES2-AcGFP1 vector (Clontech) together with the 3’ splicing elements using the restriction sites for EcoRI and PstI. The coding sequence (CDS) of the thymidine kinase gene from herpes simplex virus (HSV-tk) without the start codon was amplified from the HAX1-targeting vector [page 1058, left column, second full paragraph].
Regarding claim 34, Gruber et al. teaches an RTM construct as shown in Figure 2A (reproduced below) comprising a CMV promoter.
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Regarding claim 36, Gruber et al. teaches that RTMm2 was cloned into a retroviral vector and transduced into EB-SCC cells [page 1063, right column, first full paragraph].
Regarding claim 37, Gruber et al. teaches that semi-quantitative RT-PCR was performed to detect SLCO1B3-tk fusion transcripts in EB-SCC or HEK293AD cells co-transfected with SLCO1B3-MG and RTM [Section 2.7.].
However, Gruber et al. does not teach a HERV pre-mRNA.
Lemaitre et al. teaches that the HERV-K (HML2) family is remarkable in that it has recently amplified in humans and many of its ORFs are intact, making it the largest contributor of retroviral-derived proteins in the genome. Expression of the associated proteins and viral particles has been detected in cell lines as well as in human cancers, including melanoma, breast and ovarian cancers [page 2, second paragraph]. Lemaitre et al. also teaches that HERV-K Env activates the ERK1/2 pathway and promotes the expression of transcription factors involved in oncogenesis [page 2, last paragraph bridging to page 3].
It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RNA trans-splicing molecule of Gruber et al. wherein the binding region is specific for a HERV pre-mRNA because Gruber et al. taught RNA trans-splicing molecules (RTMs) consisting of a binding domain (BD) for gene targeting (RNA trans-splicing molecules (RTM) specifically binding the pre-mRNA of SLCO1B3), a splicing domain for efficient trans-splicing, and a coding domain comprising the sequence to be introduced, Gruber et al. taught that targeting tumor marker genes by RNA trans-splicing is a promising means to induce tumor cell-specific death, Lemaitre et al. taught that the HERV-K (HML2) family is remarkable in that it has recently amplified in humans and many of its ORFs are intact, making it the largest contributor of retroviral-derived proteins in the genome, expression of the associated proteins and viral particles has been detected in cell lines as well as in human cancers, including melanoma, breast and ovarian cancers, and Lemaitre et al. taught that HERV-K Env activates the ERK1/2 pathway and promotes the expression of transcription factors involved in oncogenesis. One would have made such a modification because Gruber et al. taught that targeting tumor marker genes by RNA trans-splicing is a promising means to induce tumor cell-specific death and thus it would have amounted to a simple substitution of one known element for another to obtain predictable results.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Gruber et al. (Molecular Oncology 2013; reference previously cited by the Examiner) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner) as applied to claims 1, 3, 10, 17, 18, 28, 34, 36, and 37 above, and further in view of Fotin-Mleczek et al. (US 2023/0338579).
Regarding claim 12, the teachings of Gruber et al. and Lemaitre et al. are discussed above.
However, Gruber et al. and Lemaitre et al. do not teach wherein the HSV thymidine kinase comprises an amino acid sequence that is a variant of SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6.
It is noted that instant SEQ ID NO: 6 (designated as Qy) positions 2 through 376 has a match to instant SEQ ID NO: 8 (designated as Db) positions 1 through 375 as shown in the alignment below with a substitution at positions 45 and 59 of SEQ ID NO: 8 which corresponds to positions 46 and 60 of SEQ ID NO: 6.
Query Match 99.4%; Score 1954; DB 1; Length 375;
Best Local Similarity 99.5%;
Matches 373; Conservative 2; Mismatches 0; Indels 0; Gaps 0;
Qy 2 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKMPTLLRVYIDGPHGMG 61
||||||||||||||||||||||||||||||||||||||||||||:|||||||||||||:|
Db 1 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKLPTLLRVYIDGPHGIG 60
Qy 62 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 120
Qy 122 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 180
Qy 182 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 240
Qy 242 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 300
Qy 302 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 360
Qy 362 CDLARTFAREMGEAN 376
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Db 361 CDLARTFAREMGEAN 375
Fotin-Mleczek et al. teaches RNA containing compositions for use in the treatment or prophylaxis of tumor and/or cancer diseases [abstract]. Fotin-Mleczek et al. SEQ ID NO: 6769 (designated as Db) positions 2 through 376 has a match to instant SEQ ID NO: 8 (designated as Qy) positions 1 through 375 with a substitution at positions 45 and 59 of SEQ ID NO: 8 as shown in the alignment below. As shown above, instant SEQ ID NO: 8 is a variant of instant SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6.
Query Match 99.7%; Score 1954; Length 376;
Best Local Similarity 99.5%;
Matches 373; Conservative 2; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKLPTLLRVYIDGPHGIG 60
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Db 2 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKMPTLLRVYIDGPHGMG 61
Qy 61 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 62 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 121
Qy 121 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 122 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 181
Qy 181 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 241
Qy 241 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 301
Qy 301 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 361
Qy 361 CDLARTFAREMGEAN 375
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Db 362 CDLARTFAREMGEAN 376
Fotin-Mleczek et al. teaches RNA sequences encoding a suicide gene product according to Table 4 [0117] such as SEQ ID NO: 6769 (protein sequence) which is associated with the gene thymidine kinase_TK as shown below [Table 4, page 23].
Gene Name Protein Accession No. Protein seq. RNA seq. wt RNA seq.
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It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RTM of Gruber et al. and Lemaitre et al. wherein the HSV thymidine kinase comprises an amino acid sequence that is a variant of SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6 because Gruber et al. and Lemaitre et al. taught an RTM comprising a binding region specific for a HERV pre-mRNA, a trans-splicing domain, and a coding sequence for a suicide protein wherein the suicide protein is Herpes simplex virus (HSV) thymidine kinase and Fotin-Mleczek et al. taught RNA sequences encoding a suicide gene product such as SEQ ID NO: 6769 which is associated with the gene thymidine kinase_TK. One of ordinary skill in the art would have made such a modification because it would have amounted to combining known prior art elements to yield predictable results.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Gruber et al. (Molecular Oncology 2013; reference previously cited by the Examiner) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner) as applied to claims 1, 3, 10, 17, 18, 28, 34, 36, and 37 above, and further in view of Lee et al. (US 2020/0270612).
Regarding claim 23, the teachings of Gruber et al. and Lemaitre et al. are discussed above.
However, Gruber et al. and Lemaitre et al. do not teach wherein the RTM comprises a variant of SEQ ID NO: 15.
Lee et al. teaches a cancer-specific trans-splicing ribozyme and a use thereof [abstract]. Lee et al. teaches that a drug-sensitizing gene is a gene encoding an enzyme that converts a non-toxic prodrug into a toxic material, and since cells into which the gene is introduced die, it is also called a suicide gene. When a non-toxic prodrug is systemically administered to normal cells, the prodrug is converted into a toxic metabolite only in cancer cells to change sensitization to a drug, resulting in the destruction of cancer cells. Such a drug-sensitizing gene is preferably a herpes simplex virus-thymidine kinase (HSVtk) gene using ganciclovir as a prodrug, or a cytosine deaminase (CD) gene of E. coli using 5-fluorocytosine (5-FC) as a prodrug, and most preferably, a HSVtk gene including a sequence of SEQ ID NO: 4 [0118]. The sequence alignment of Lee et al. SEQ ID NO: 4 (designated as Db) and instant SEQ ID NO: 15 (designated as Qy) is shown below.
Query Match 63.1%; Score 953; Length 1131;
Best Local Similarity 73.0%;
Matches 920; Conservative 188; Mismatches 20; Indels 133; Gaps 1;
Qy 245 GCUUCGUACCCCUGCCAUCAACACGCGUCUGCGUUCGACCAGGCGGCGCGAUCACGGGGA 304
||::||:|||||:||||:|||||||||:|:|||::||||||||| ||||| :| || ||
Db 4 GCTTCGTACCCCTGCCATCAACACGCGTCTGCGTTCGACCAGGCTGCGCGTTCTCGCGGC 63
Qy 305 CACAGCAACCGACGGACGGCGUUGCGCCCUCGCCGGCAGCAAGAAGCCACGGAAGUCCGC 364
|| ||||||||||| ||||||::||||||:|||||||||||||||||||||||||:||||
Db 64 CATAGCAACCGACGTACGGCGTTGCGCCCTCGCCGGCAGCAAGAAGCCACGGAAGTCCGC 123
Qy 365 CCGGAGCAGAAACUGCCCACGCUACUGCGGGUUUAUAUAGACGGUCCCCACGGGAUCGGG 424
| |||||||||| :||||||||:||:|||||:::|:|:||||||:|| |||||||: |||
Db 124 CTGGAGCAGAAAATGCCCACGCTACTGCGGGTTTATATAGACGGTCCTCACGGGATGGGG 183
Qy 425 AAAACCACCACCACGCAACUGCUGGUGGCCCUGGGUUCGCGCGACGAUAUCGUCUACGUA 484
|||||||||||||||||||:||:||:|||||:|||::||||||||||:|:||:|:|||:|
Db 184 AAAACCACCACCACGCAACTGCTGGTGGCCCTGGGTTCGCGCGACGATATCGTCTACGTA 243
Qy 485 CCCGAGCCGAUGACUUACUGGCGGGUGCUGGGGGCUUCCGAGACAAUCGCGAACAUCUAC 544
||||||||||:|||::||:||| ||:||:||||||::|||||||||:||||||||:|:||
Db 244 CCCGAGCCGATGACTTACTGGCAGGTGCTGGGGGCTTCCGAGACAATCGCGAACATCTAC 303
Qy 545 ACCACACAACACCGCCUCGACCAGGUAAGUAUCAAGGUUACAAGACAGGUUUAAGGAGAC 604
||||||||||||||||:||||
Db 304 ACCACACAACACCGCCTCGAC--------------------------------------- 324
Qy 605 CAAUAGAAACUGGGCUUGUCGAGACAGAGACGACUCUUGCGUUUCUGAUAGGCACCUAUU 664
Db 325 ------------------------------------------------------------ 324
Qy 665 GGUCUUACUGACAUCCACUUUGCCUUUCUCUCCACAGGGUGAGAUAUCGGCCGGGGACGC 724
|||||:||||:|:|||||||||||||
Db 325 ----------------------------------CAGGGTGAGATATCGGCCGGGGACGC 350
Qy 725 GGCGGUGGUAAUGACAAGCGCCCAGAUAACAAUGGGCAUGCCUUAUGCCGUGACCGACGC 784
|||||:||:||:||||||||||||||:|||||:|||||:|||::|:||||:|||||||||
Db 351 GGCGGTGGTAATGACAAGCGCCCAGATAACAATGGGCATGCCTTATGCCGTGACCGACGC 410
Qy 785 CGUUCUGGCUCCUCAUAUCGGGGGGGAGGCUGGGAGCUCACAUGCCCCUCCUCCGGCCCU 844
||::|:|||:||:||:|:||||||||||||:||||||:||||:||||| || |||||||:
Db 411 CGTTCTGGCTCCTCATATCGGGGGGGAGGCTGGGAGCTCACATGCCCCGCCCCCGGCCCT 470
Qy 845 CACCCUCAUCUUCGACCGCCAUCCCAUCGCCGCCCUCCUGUGCUACCCGGCCGCGCGAUA 904
|||||:||:|::|||||||||:||||:||||||||:||:|:||:||||||||||||||:|
Db 471 CACCCTCATCTTCGACCGCCATCCCATCGCCGCCCTCCTGTGCTACCCGGCCGCGCGATA 530
Qy 905 CCUUAUGGGCAGCAUGACCCCCCAGGCCGUGCUGGCGUUCGUGGCCCUCAUCCCGCCGAC 964
||::|:||||||||:||||||||||||||:||:||||::||:|||||:||:|||||||||
Db 531 CCTTATGGGCAGCATGACCCCCCAGGCCGTGCTGGCGTTCGTGGCCCTCATCCCGCCGAC 590
Qy 965 CUUGCCCGGCACAAACAUCGUGUUGGGGGCCCUUCCGGAGGACAGACACAUCGACCGCCU 1024
|::||||||||||||||:||:|::||||||||::||||||||||||||||:||||||||:
Db 591 CTTGCCCGGCACAAACATCGTGTTGGGGGCCCTTCCGGAGGACAGACACATCGACCGCCT 650
Qy 1025 GGCCAAACGCCAGCGCCCCGGCGAGCGGCUUGACCUGGCUAUGCUGGCCGCGAUUCGCCG 1084
|||||||||||||||||||||||||||||::||||:|||:|:||:||||||||::|||||
Db 651 GGCCAAACGCCAGCGCCCCGGCGAGCGGCTTGACCTGGCTATGCTGGCCGCGATTCGCCG 710
Qy 1085 CGUUUACGGGCUGCUUGCCAAUACGGUGCGGUAUCUGCAGGGCGGCGGGUCGUGGCGGGA 1144
||:::||||||:||::|||||:||||:||||:|:|:|||||||||||||:||:|||||||
Db 711 CGTTTACGGGCTGCTTGCCAATACGGTGCGGTATCTGCAGGGCGGCGGGTCGTGGCGGGA 770
Qy 1145 GGAUUGGGGACAGCUUUCGGGGACGGCCGUGCCGCCUCAGGGUGCCGAGCCUCAGAGCAA 1204
|||::|||||||||:::||||||||||||:|||||| |||||:|||||||| ||||||||
Db 771 GGATTGGGGACAGCTTTCGGGGACGGCCGTGCCGCCCCAGGGTGCCGAGCCCCAGAGCAA 830
Qy 1205 CGCGGGCCCACGACCCCAUAUCGGGGACACGUUAUUUACCCUGUUUCGGGCCCCCGAGUU 1264
||||||||||||||||||:|:||||||||||::|:::||||:|:::||||||||||||::
Db 831 CGCGGGCCCACGACCCCATATCGGGGACACGTTATTTACCCTGTTTCGGGCCCCCGAGTT 890
Qy 1265 GCUGGCCCCCAACGGCGACCUGUAUAACGUGUUUGCCUGGGCCUUGGACGUCUUGGCCAA 1324
||:|||||||||||||||||:|:| ||||:|:::|||:|||||::|||||:|::||||||
Db 891 GCTGGCCCCCAACGGCGACCTGTACAACGTGTTTGCCTGGGCCTTGGACGTCTTGGCCAA 950
Qy 1325 ACGCCUCCGUCCCAUGCACGUCUUUAUCCUGGAUUACGACCAAUCGCCCGCCGGCUGCCG 1384
|||||:|||:||||:|||||:|:::|:||:|||::||||||||:|||||||||||:||||
Db 951 ACGCCTCCGTCCCATGCACGTCTTTATCCTGGATTACGACCAATCGCCCGCCGGCTGCCG 1010
Qy 1385 GGACGCCCUGCUGCAACUUACCUCCGGGAUGGUCCAGACCCACGUCACCACCCCAGGCUC 1444
||||||||:||:|||||::|||:||||||:||:|||||||||||:||||||||| |||:|
Db 1011 GGACGCCCTGCTGCAACTTACCTCCGGGATGGTCCAGACCCACGTCACCACCCCCGGCTC 1070
Qy 1445 CAUACCGACGAUCUGCGACCUGGCGCGCACGUUUGCGCGGGAGAUGGGGGAGGCGAACUG 1504
||:||||||||:|:||||||:||||||||||:::|| |||||||:||||||||| |||:|
Db 1071 CATACCGACGATCTGCGACCTGGCGCGCACGTTTGCCCGGGAGATGGGGGAGGCTAACTG 1130
Qy 1505 A 1505
|
Db 1131 A 1131
It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RTM of Gruber et al. and Lemaitre et al. wherein the RTM comprises a variant of SEQ ID NO: 15 because Gruber et al. and Lemaitre et al. taught an RTM comprising a binding region specific for a HERV pre-mRNA, a trans-splicing domain, and a coding sequence for a suicide protein, Lee et al. taught that a drug-sensitizing gene is a gene encoding an enzyme that converts a non-toxic prodrug into a toxic material, and since cells into which the gene is introduced die, it is also called a suicide gene, and Lee et al. taught that a drug-sensitizing gene is preferably a herpes simplex virus-thymidine kinase (HSVtk) gene including a sequence of SEQ ID NO: 4. One of ordinary skill in the art would have made such a modification because it would have amounted to combining known prior art elements to yield predictable results.
Claims 1, 3, 10, 17, 18, 20, 24, 25, 26, 27, 28, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Poddar et al. (Molecular Therapy: Nucleic Acids 2018) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner).
Regarding claims 1, 3, 17, 24, 25, and 28, Poddar et al. teaches that the specificity of
trans-splicing with the intended target splice site was improved 10-fold by designing tsRNA that harbors secondary target binding domains shielding alternative on-target and blinding off-target splicing events. Such rationally designed suicide RNAs efficiently triggered death of HPV-16-transduced or hepatoblastoma-derived human tissue culture cells without evidence for off-target cell killing [abstract]. Poddar et al. teaches the design of tsRNA for 5’ exon replacement (ER) (claim 24) and 3’ exon replacement (ER) (claim 17) as shown in Figure 1A (reproduced below):
PNG
media_image9.png
548
866
media_image9.png
Greyscale
The 5’ ER tsRNA comprises in a 5’ to 3’ direction the HSVtk coding sequence, the trans-splicing domain, and the binding region for a pre-mRNA [Figure 1A] (claim 24). The trans-splicing domain of the 5’ ER tsRNA comprises a splice donor and intronic splice enhancer (ISE) [Figure 1A] (claim 25).
The 3’ ER tsRNA comprises in a 5’ to 3’ direction the binding region, the trans-splicing domain, and the HSVtk coding sequence [Figure 1A] (claim 17).
Regarding claims 10 and 26, Figure 1A also shows that the HSVtk coding domain occurs with a start codon for 5’ ER.
Regarding claim 18, Figure 1A shows that the splicing domain of the 3’ ER comprises “AG” which is an acceptor site.
Regarding claim 20, Poddar et al. teaches that the tsRNA for 3’ ER was featured with the 2A peptide derived from porcine teschovirus-1 (P2A) proteolytic cleavage site positioned downstream of the splice A site to trigger proteolytic release of the HSVTK from the chimeric fusion protein, which results from the 3’ ER trans-splice reaction [page 42, left column, first full paragraph].
Regarding claim 27, Poddar et al. also teaches that the tsRNA for 5’ ER was furnished with a tertiary structure-stabilized hammerhead ribozyme (HHRz) positioned downstream of the BD. The HHRz could then crop itself, together with the simian virus 40 (SV40) poly(A) site, to trigger nuclear RNA retention and to avoid trans-splicing-independent HSVTK expression [page 42, left column, first full paragraph].
Regarding claim 34, Poddar et al. teaches a tsRNA construct as shown in Figure 1A comprising a CMV promoter.
However, Poddar et al. does not teach a binding region specific for a HERV pre-mRNA (claim 1) wherein the HERV pre-mRNA is a HERV-K pre-mRNA (claim 3).
Lemaitre et al. teaches that the HERV-K (HML2) family is remarkable in that it has recently amplified in humans and many of its ORFs are intact, making it the largest contributor of retroviral-derived proteins in the genome. Expression of the associated proteins and viral particles has been detected in cell lines as well as in human cancers, including melanoma, breast and ovarian cancers [page 2, second paragraph]. Lemaitre et al. also teaches that HERV-K Env activates the ERK1/2 pathway and promotes the expression of transcription factors involved in oncogenesis [page 2, last paragraph bridging to page 3].
It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RNA trans-splicing molecule (RTM) of Poddar et al. wherein the binding region is specific for a HERV pre-mRNA because Poddar et al. taught an RTM comprising a binding region, a trans-splicing domain, and a coding sequence, Poddar et al. taught that the specificity of trans-splicing with the intended target splice site was improved 10-fold by designing tsRNA that harbors secondary target binding domains shielding alternative on-target and blinding off-target splicing events and such rationally designed suicide RNAs efficiently triggered death of HPV-16-transduced or hepatoblastoma-derived human tissue culture cells without evidence for off-target cell killing, Lemaitre et al. taught that the HERV-K (HML2) family is remarkable in that it has recently amplified in humans and many of its ORFs are intact, making it the largest contributor of retroviral-derived proteins in the genome, expression of the associated proteins and viral particles has been detected in cell lines as well as in human cancers, including melanoma, breast and ovarian cancers, and Lemaitre et al. taught that HERV-K Env activates the ERK1/2 pathway and promotes the expression of transcription factors involved in oncogenesis. One would have made such a modification because Poddar et al. taught that the specificity of trans-splicing with the intended target splice site was improved 10-fold by designing tsRNA that harbors secondary target binding domains shielding alternative on-target and blinding off-target splicing events and thus it would have amounted to a simple substitution of one known element for another to obtain predictable results.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Poddar et al. (Molecular Therapy: Nucleic Acids 2018) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner) as applied to claims 1, 3, 10, 17, 18, 20, 24, 25, 26, 27, 28, and 34 above, and further in view of Fotin-Mleczek et al. (US 2023/0338579).
Regarding claim 12, the teachings of Poddar et al. and Lemaitre et al. are discussed above.
However, Poddar et al. and Lemaitre et al. do not teach wherein the HSV thymidine kinase comprises an amino acid sequence that is a variant of SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6.
It is noted that instant SEQ ID NO: 6 (designated as Qy) positions 2 through 376 has a match to instant SEQ ID NO: 8 (designated as Db) positions 1 through 375 as shown in the alignment below with a substitution at positions 45 and 59 of SEQ ID NO: 8 which corresponds to positions 46 and 60 of SEQ ID NO: 6.
Query Match 99.4%; Score 1954; DB 1; Length 375;
Best Local Similarity 99.5%;
Matches 373; Conservative 2; Mismatches 0; Indels 0; Gaps 0;
Qy 2 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKMPTLLRVYIDGPHGMG 61
||||||||||||||||||||||||||||||||||||||||||||:|||||||||||||:|
Db 1 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKLPTLLRVYIDGPHGIG 60
Qy 62 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 120
Qy 122 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 180
Qy 182 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 240
Qy 242 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 300
Qy 302 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 360
Qy 362 CDLARTFAREMGEAN 376
|||||||||||||||
Db 361 CDLARTFAREMGEAN 375
Fotin-Mleczek et al. teaches RNA containing compositions for use in the treatment or prophylaxis of tumor and/or cancer diseases [abstract]. Fotin-Mleczek et al. SEQ ID NO: 6769 (designated as Db) positions 2 through 376 has a match to instant SEQ ID NO: 8 (designated as Qy) positions 1 through 375 with a substitution at positions 45 and 59 of SEQ ID NO: 8 as shown in the alignment below. As shown above, instant SEQ ID NO: 8 is a variant of instant SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6.
Query Match 99.7%; Score 1954; Length 376;
Best Local Similarity 99.5%;
Matches 373; Conservative 2; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKLPTLLRVYIDGPHGIG 60
||||||||||||||||||||||||||||||||||||||||||||:|||||||||||||:|
Db 2 ASYPCHQHASAFDQAARSRGHSNRRTALRPRRQQEATEVRPEQKMPTLLRVYIDGPHGMG 61
Qy 61 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 62 KTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVM 121
Qy 121 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 122 TSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGS 181
Qy 181 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 MTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGL 241
Qy 241 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 LANTVRYLQGGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPN 301
Qy 301 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 GDLYNVFAWALDVLAKRLRPMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTI 361
Qy 361 CDLARTFAREMGEAN 375
|||||||||||||||
Db 362 CDLARTFAREMGEAN 376
Fotin-Mleczek et al. teaches RNA sequences encoding a suicide gene product according to Table 4 [0117] such as SEQ ID NO: 6769 (protein sequence) which is associated with the gene thymidine kinase_TK as shown below [Table 4, page 23].
Gene Name Protein Accession No. Protein seq. RNA seq. wt RNA seq.
PNG
media_image8.png
38
670
media_image8.png
Greyscale
It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RTM of Poddar et al. and Lemaitre et al. wherein the HSV thymidine kinase comprises an amino acid sequence that is a variant of SEQ ID NO: 6 with modifications relative to SEQ ID NO: 6 at positions corresponding to positions 46 and 60 of SEQ ID NO: 6 because Poddar et al. and Lemaitre et al. taught an RTM comprising a binding region specific for a HERV pre-mRNA, a trans-splicing domain, and a coding sequence for a suicide protein wherein the suicide protein is Herpes simplex virus (HSV) thymidine kinase and Fotin-Mleczek et al. taught RNA sequences encoding a suicide gene product such as SEQ ID NO: 6769 which is associated with the gene thymidine kinase_TK. One of ordinary skill in the art would have made such a modification because it would have amounted to combining known prior art elements to yield predictable results.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Poddar et al. (Molecular Therapy: Nucleic Acids 2018) in view of Lemaitre et al. (PLoS Pathogens 2017; reference previously cited by the Examiner) as applied to claims 1, 3, 10, 17, 18, 20, 24, 25, 26, 27, 28, and 34 above, and further in view of Lee et al. (US 2020/0270612).
Regarding claim 23, the teachings of Poddar et al. and Lemaitre et al. are discussed above.
However, Poddar et al. and Lemaitre et al. do not teach wherein the RTM comprises a variant of SEQ ID NO: 15.
Lee et al. teaches a cancer-specific trans-splicing ribozyme and a use thereof [abstract]. Lee et al. teaches that a drug-sensitizing gene is a gene encoding an enzyme that converts a non-toxic prodrug into a toxic material, and since cells into which the gene is introduced die, it is also called a suicide gene. When a non-toxic prodrug is systemically administered to normal cells, the prodrug is converted into a toxic metabolite only in cancer cells to change sensitization to a drug, resulting in the destruction of cancer cells. Such a drug-sensitizing gene is preferably a herpes simplex virus-thymidine kinase (HSVtk) gene using ganciclovir as a prodrug, or a cytosine deaminase (CD) gene of E. coli using 5-fluorocytosine (5-FC) as a prodrug, and most preferably, a HSVtk gene including a sequence of SEQ ID NO: 4 [0118]. The sequence alignment of Lee et al. SEQ ID NO: 4 (designated as Db) and instant SEQ ID NO: 15 (designated as Qy) is shown below.
Query Match 63.1%; Score 953; Length 1131;
Best Local Similarity 73.0%;
Matches 920; Conservative 188; Mismatches 20; Indels 133; Gaps 1;
Qy 245 GCUUCGUACCCCUGCCAUCAACACGCGUCUGCGUUCGACCAGGCGGCGCGAUCACGGGGA 304
||::||:|||||:||||:|||||||||:|:|||::||||||||| ||||| :| || ||
Db 4 GCTTCGTACCCCTGCCATCAACACGCGTCTGCGTTCGACCAGGCTGCGCGTTCTCGCGGC 63
Qy 305 CACAGCAACCGACGGACGGCGUUGCGCCCUCGCCGGCAGCAAGAAGCCACGGAAGUCCGC 364
|| ||||||||||| ||||||::||||||:|||||||||||||||||||||||||:||||
Db 64 CATAGCAACCGACGTACGGCGTTGCGCCCTCGCCGGCAGCAAGAAGCCACGGAAGTCCGC 123
Qy 365 CCGGAGCAGAAACUGCCCACGCUACUGCGGGUUUAUAUAGACGGUCCCCACGGGAUCGGG 424
| |||||||||| :||||||||:||:|||||:::|:|:||||||:|| |||||||: |||
Db 124 CTGGAGCAGAAAATGCCCACGCTACTGCGGGTTTATATAGACGGTCCTCACGGGATGGGG 183
Qy 425 AAAACCACCACCACGCAACUGCUGGUGGCCCUGGGUUCGCGCGACGAUAUCGUCUACGUA 484
|||||||||||||||||||:||:||:|||||:|||::||||||||||:|:||:|:|||:|
Db 184 AAAACCACCACCACGCAACTGCTGGTGGCCCTGGGTTCGCGCGACGATATCGTCTACGTA 243
Qy 485 CCCGAGCCGAUGACUUACUGGCGGGUGCUGGGGGCUUCCGAGACAAUCGCGAACAUCUAC 544
||||||||||:|||::||:||| ||:||:||||||::|||||||||:||||||||:|:||
Db 244 CCCGAGCCGATGACTTACTGGCAGGTGCTGGGGGCTTCCGAGACAATCGCGAACATCTAC 303
Qy 545 ACCACACAACACCGCCUCGACCAGGUAAGUAUCAAGGUUACAAGACAGGUUUAAGGAGAC 604
||||||||||||||||:||||
Db 304 ACCACACAACACCGCCTCGAC--------------------------------------- 324
Qy 605 CAAUAGAAACUGGGCUUGUCGAGACAGAGACGACUCUUGCGUUUCUGAUAGGCACCUAUU 664
Db 325 ------------------------------------------------------------ 324
Qy 665 GGUCUUACUGACAUCCACUUUGCCUUUCUCUCCACAGGGUGAGAUAUCGGCCGGGGACGC 724
|||||:||||:|:|||||||||||||
Db 325 ----------------------------------CAGGGTGAGATATCGGCCGGGGACGC 350
Qy 725 GGCGGUGGUAAUGACAAGCGCCCAGAUAACAAUGGGCAUGCCUUAUGCCGUGACCGACGC 784
|||||:||:||:||||||||||||||:|||||:|||||:|||::|:||||:|||||||||
Db 351 GGCGGTGGTAATGACAAGCGCCCAGATAACAATGGGCATGCCTTATGCCGTGACCGACGC 410
Qy 785 CGUUCUGGCUCCUCAUAUCGGGGGGGAGGCUGGGAGCUCACAUGCCCCUCCUCCGGCCCU 844
||::|:|||:||:||:|:||||||||||||:||||||:||||:||||| || |||||||:
Db 411 CGTTCTGGCTCCTCATATCGGGGGGGAGGCTGGGAGCTCACATGCCCCGCCCCCGGCCCT 470
Qy 845 CACCCUCAUCUUCGACCGCCAUCCCAUCGCCGCCCUCCUGUGCUACCCGGCCGCGCGAUA 904
|||||:||:|::|||||||||:||||:||||||||:||:|:||:||||||||||||||:|
Db 471 CACCCTCATCTTCGACCGCCATCCCATCGCCGCCCTCCTGTGCTACCCGGCCGCGCGATA 530
Qy 905 CCUUAUGGGCAGCAUGACCCCCCAGGCCGUGCUGGCGUUCGUGGCCCUCAUCCCGCCGAC 964
||::|:||||||||:||||||||||||||:||:||||::||:|||||:||:|||||||||
Db 531 CCTTATGGGCAGCATGACCCCCCAGGCCGTGCTGGCGTTCGTGGCCCTCATCCCGCCGAC 590
Qy 965 CUUGCCCGGCACAAACAUCGUGUUGGGGGCCCUUCCGGAGGACAGACACAUCGACCGCCU 1024
|::||||||||||||||:||:|::||||||||::||||||||||||||||:||||||||:
Db 591 CTTGCCCGGCACAAACATCGTGTTGGGGGCCCTTCCGGAGGACAGACACATCGACCGCCT 650
Qy 1025 GGCCAAACGCCAGCGCCCCGGCGAGCGGCUUGACCUGGCUAUGCUGGCCGCGAUUCGCCG 1084
|||||||||||||||||||||||||||||::||||:|||:|:||:||||||||::|||||
Db 651 GGCCAAACGCCAGCGCCCCGGCGAGCGGCTTGACCTGGCTATGCTGGCCGCGATTCGCCG 710
Qy 1085 CGUUUACGGGCUGCUUGCCAAUACGGUGCGGUAUCUGCAGGGCGGCGGGUCGUGGCGGGA 1144
||:::||||||:||::|||||:||||:||||:|:|:|||||||||||||:||:|||||||
Db 711 CGTTTACGGGCTGCTTGCCAATACGGTGCGGTATCTGCAGGGCGGCGGGTCGTGGCGGGA 770
Qy 1145 GGAUUGGGGACAGCUUUCGGGGACGGCCGUGCCGCCUCAGGGUGCCGAGCCUCAGAGCAA 1204
|||::|||||||||:::||||||||||||:|||||| |||||:|||||||| ||||||||
Db 771 GGATTGGGGACAGCTTTCGGGGACGGCCGTGCCGCCCCAGGGTGCCGAGCCCCAGAGCAA 830
Qy 1205 CGCGGGCCCACGACCCCAUAUCGGGGACACGUUAUUUACCCUGUUUCGGGCCCCCGAGUU 1264
||||||||||||||||||:|:||||||||||::|:::||||:|:::||||||||||||::
Db 831 CGCGGGCCCACGACCCCATATCGGGGACACGTTATTTACCCTGTTTCGGGCCCCCGAGTT 890
Qy 1265 GCUGGCCCCCAACGGCGACCUGUAUAACGUGUUUGCCUGGGCCUUGGACGUCUUGGCCAA 1324
||:|||||||||||||||||:|:| ||||:|:::|||:|||||::|||||:|::||||||
Db 891 GCTGGCCCCCAACGGCGACCTGTACAACGTGTTTGCCTGGGCCTTGGACGTCTTGGCCAA 950
Qy 1325 ACGCCUCCGUCCCAUGCACGUCUUUAUCCUGGAUUACGACCAAUCGCCCGCCGGCUGCCG 1384
|||||:|||:||||:|||||:|:::|:||:|||::||||||||:|||||||||||:||||
Db 951 ACGCCTCCGTCCCATGCACGTCTTTATCCTGGATTACGACCAATCGCCCGCCGGCTGCCG 1010
Qy 1385 GGACGCCCUGCUGCAACUUACCUCCGGGAUGGUCCAGACCCACGUCACCACCCCAGGCUC 1444
||||||||:||:|||||::|||:||||||:||:|||||||||||:||||||||| |||:|
Db 1011 GGACGCCCTGCTGCAACTTACCTCCGGGATGGTCCAGACCCACGTCACCACCCCCGGCTC 1070
Qy 1445 CAUACCGACGAUCUGCGACCUGGCGCGCACGUUUGCGCGGGAGAUGGGGGAGGCGAACUG 1504
||:||||||||:|:||||||:||||||||||:::|| |||||||:||||||||| |||:|
Db 1071 CATACCGACGATCTGCGACCTGGCGCGCACGTTTGCCCGGGAGATGGGGGAGGCTAACTG 1130
Qy 1505 A 1505
|
Db 1131 A 1131
It would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the RTM of Poddar et al. and Lemaitre et al. wherein the RTM comprises a variant of SEQ ID NO: 15 because Poddar et al. and Lemaitre et al. taught an RTM comprising a binding region specific for a HERV pre-mRNA, a trans-splicing domain, and a coding sequence for a suicide protein, Lee et al. taught that a drug-sensitizing gene is a gene encoding an enzyme that converts a non-toxic prodrug into a toxic material, and since cells into which the gene is introduced die, it is also called a suicide gene, and Lee et al. taught that a drug-sensitizing gene is preferably a herpes simplex virus-thymidine kinase (HSVtk) gene including a sequence of SEQ ID NO: 4. One of ordinary skill in the art would have made such a modification because it would have amounted to combining known prior art elements to yield predictable results.
Conclusion
No claims are allowed.
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/C.T./
Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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